Merge branch 'master' into 'master'

Split Hull Bug Fix

There was a bug in splitting hulls where the new hulls did not retain their pixel lists.  This has now been fixed.

Please allow this fix to be merged.

src/c/Material.cpp

@@ -282,8 +282,8 @@ void createStaticVolumeShaderText(std::string strChans)
 	shaderText += "\n";
 	shaderText += "struct PixelOutputType\n";
 	shaderText += "{\n";
-	shaderText += "	float4 color : SV_TARGET;\n";
-	shaderText += "	float depth : SV_DEPTH;\n";
+	shaderText += "\tfloat4 color : SV_TARGET;\n";
+	shaderText += "\tfloat depth : SV_DEPTH;\n";
 	shaderText += "};\n";
 	shaderText += "\n";
 	shaderText += "Texture3D    g_txDiffuse[" + strChans + "] : register( t0 );\n";
@@ -303,14 +303,26 @@ void createStaticVolumeShaderText(std::string strChans)
 	shaderText += "\tfloat alpha = 0.0f;\n";
 	shaderText += "\n";
 	shaderText += "\tfloat4 mainLightDir = float4(-0.5774,-0.5774,0.5774,0);\n";
-	shaderText += "\tfloat unlitComposite = 0.0f;\n";
+	shaderText += "\tfloat3 unlitComposite = float3(0.0f,0.0f,0.0f);\n";
+	shaderText += "\tfloat3 alphaComposite = float3(0.0f,0.0f,0.0f);\n";
+	shaderText += "\n";
 	shaderText += "\tint numAlpha = 0;\n";
 	shaderText += "\tfloat3 grad;\n";
+	shaderText += "\n";
+	shaderText += "float maxIntensity = 0;\n";
+	shaderText += "\n";
 	shaderText += "\t[unroll(" + strChans + ")] for (int i=0; i<" + strChans + "; ++i)\n";
 	shaderText += "\t{\n";
 	shaderText += "\t\tfloat intensity = g_txDiffuse[i].Sample( g_samLinear[i], input.TextureUV );\n";
 	shaderText += "\t\tintensity = clamp(intensity,ranges[i][0],ranges[i][1]);\n";
 	shaderText += "\t\tintensity = transferFunctions[i][0]*intensity*intensity+transferFunctions[i][1]*intensity+transferFunctions[i][2];\n";
+	shaderText += "\t\tif (intensity < 0.2f || channelColor[i].a < 0.01f)\n";
+	shaderText += "\t\t{\n";
+	shaderText += "\t\t\tintensity = 0;\n";
+	shaderText += "\t\t}\n";
+	//shaderText += "\t\tmaxIntensity = max(intensity*channelColor[i].a,maxIntensity);\n";
+	shaderText += "\t\tmaxIntensity = max(intensity,maxIntensity);\n";
+	shaderText += "\n";
 	shaderText += "\t\tfloat lightMod = 1.0f;\n";
 	shaderText += "\t\tif(lightOn.x>0)\n";
 	shaderText += "\t\t{\n";
@@ -321,24 +333,29 @@ void createStaticVolumeShaderText(std::string strChans)
 	shaderText += "\t\t\tgrad.z = g_txDiffuse[i].Sample(g_samLinear[i], input.TextureUV+gradientSampleDirection[2]) - \n";
 	shaderText += "\t\t\t\tg_txDiffuse[i].Sample(g_samLinear[i], input.TextureUV-gradientSampleDirection[2]);\n";
 	shaderText += "\t\t\tgrad = normalize(grad);\n";
-	shaderText += "\t\t\tlightMod = saturate(dot(grad,mainLightDir)*2.0)*0.7 + 0.3;\n";
+	shaderText += "\t\t\tlightMod = saturate(dot(grad,mainLightDir)*2.0)*0.65 + 0.35;\n";
 	shaderText += "\t\t}\n";
-	shaderText += "\t\tif (channelColor[i].a>0)\n";
-	shaderText += "\t\t\t++numAlpha;\n";
 	shaderText += "\n";
-	shaderText += "\t\talpha +=  channelColor[i].a;\n";
-	shaderText += "\t\toutput.color.rgb += (lightMod*intensity*channelColor[i].rgb*channelColor[i].a);\n";
-	shaderText += "\t\tunlitComposite += intensity*channelColor[i].a;\n";
+	shaderText += "\t\toutput.color.rgb += (lightMod*intensity*channelColor[i].rgb);\n";
+	shaderText += "\t\tunlitComposite += intensity*channelColor[i].rgb;\n";
+	shaderText += "\t\talphaComposite += intensity*channelColor[i].rgb*channelColor[i].a;\n";
 	shaderText += "\t}\n";
-	shaderText += "\tif (alpha!=0)\n";
+	shaderText += "\n";
+	shaderText += "\tfloat maxComponent = max(max(unlitComposite.r,unlitComposite.g),unlitComposite.b);\n";
+	shaderText += "\tfloat maxAplha = max(max(alphaComposite.r,alphaComposite.g),alphaComposite.b);\n";
+	shaderText += "\tif (maxComponent!=0)\n";
+	shaderText += "\t{\n";
+	shaderText += "\t\toutput.color.rgb /= maxComponent;\n";
+	shaderText += "\t\toutput.color.rgb *= maxIntensity;\n";
+	shaderText += "\t}\n";
+	shaderText += "\tif (maxAplha!=0)\n";
 	shaderText += "\t{\n";
-	shaderText += "\t\toutput.color.rgb /= alpha;\n";
-	shaderText += "\t\toutput.color.rgb = saturate(output.color.rgb*numAlpha*0.5f);\n";
-	shaderText += "\t\tunlitComposite /= alpha;\n";
-	shaderText += "\t\toutput.color.a = alpha / numAlpha;\n";
+	shaderText += "\t\toutput.color.a = maxAplha;\n";
+	shaderText += "\t}else{\n";
+	shaderText += "\t\toutput.color.a = 0;\n";
 	shaderText += "\t}\n";
-	shaderText += "\toutput.color.a *= saturate(unlitComposite);\n";
-	shaderText += "\toutput.color.a = output.color.a*step(0.15,output.color.a);\n";
+	shaderText += "\n";
+	shaderText += "\n";
 	shaderText += "\tif(lightOn.y>0)\n";
 	shaderText += "\t{\n";
 	shaderText += "\t\tfloat distMult = (input.Dpth.z<=0) ? (1) : (1-input.Dpth.z);\n";

src/matlab/CreateHulls.m

@@ -26,7 +26,7 @@
 %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-function [ newHulls ] = CreateHulls(bwIm, orgIm, minCellDia, frame, minXY, minZ)
+function [ newHulls ] = CreateHulls(bwIm, orgIm, minCellDia, frame, minXY, minZ, labeledIm)
 global imageData
 
 newHulls = [];
@@ -37,6 +37,9 @@ end
 if ~exist('minZ','var')
     minZ = 0;
 end
+if ~exist('labeledIm','var')
+    labeledIm = 0;
+end
 
 [newHulls,~,~] = GetEmptyStructs();
 imageDims = [imageData.XDimension, imageData.YDimension, imageData.ZDimension];
@@ -45,7 +48,12 @@ scaleFactor  =  imageDims ./ max(imageDims) .* physDims/physDims(1);
 imDiv = imageDims /2;
 minCellVol = (4*pi*(minCellDia/2)^3)/3;
 
-stts = regionprops(bwIm,orgIm,'BoundingBox','PixelList','WeightedCentroid');
+if (labeledIm==0)
+    cc = bwconncomp(bwIm);
+else
+    cc = bwIm;
+end
+stts = regionprops(cc,orgIm,'BoundingBox','PixelList','WeightedCentroid');
 if isempty(stts)
     return
 end

src/matlab/SplitHull.m

@@ -35,7 +35,7 @@ for i=1:k
     im(idx) = i;
 end
 
-newHulls = CreateHulls(im,orgImage(:,:,:,hullChan,Hulls(hull).frame),1,Hulls(hull).frame);
+newHulls = CreateHulls(im,orgImage(:,:,:,hullChan,Hulls(hull).frame),1,Hulls(hull).frame,0,0,1);
 
 oldHull = Hulls(hull);
 Hulls(hull) = newHulls(1);